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== Human Gene/Genome Annotations ==
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== Google DataSet Search Engine ==
 +
*[https://toolbox.google.com/datasetsearch Google Dataset Search]
 +
== Gene/Genome Annotations ==
 
*[http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi CCDS] The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation  
 
*[http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi CCDS] The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation  
 
*[http://www.gencodegenes.org/ GENCODE] The Encyclopedia of Genes
 
*[http://www.gencodegenes.org/ GENCODE] The Encyclopedia of Genes
  
== Human Variome Resources ==
+
== Variome Resources ==
 
- Variation DBs
 
- Variation DBs
 
*[http://exac.broadinstitute.org/ ExAC (Exome Aggregation Consortium)] Exome variation data from >60k individuals  
 
*[http://exac.broadinstitute.org/ ExAC (Exome Aggregation Consortium)] Exome variation data from >60k individuals  
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*[https://hgv.figshare.com/?WT.mc_id=BAN_HGV_database HGV Database] The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation
 
*[https://hgv.figshare.com/?WT.mc_id=BAN_HGV_database HGV Database] The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation
  
- Variant functional effect estimation
+
- Functional significance of variants
 
*[http://www.columbia.edu/~ii2135/eigen.html Eigen] Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration)
 
*[http://www.columbia.edu/~ii2135/eigen.html Eigen] Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration)
 
*[http://cadd.gs.washington.edu/home CADD: Combined Annotation Dependent Depletion] a tool for scoring the deleteriousness of SNV and indels (human only, supervised integration)
 
*[http://cadd.gs.washington.edu/home CADD: Combined Annotation Dependent Depletion] a tool for scoring the deleteriousness of SNV and indels (human only, supervised integration)
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*[http://www.broadinstitute.org/mammals/haploreg HaplogReg] Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab)
 
*[http://www.broadinstitute.org/mammals/haploreg HaplogReg] Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab)
  
== Human Genotype-to-Phenotype Resources ==
+
== Phenome/Diseasome Resources ==
 +
- Human Disease DBs
 +
*[http://www.disgenet.org/web/DisGeNET DisGeNET] MetaDB for disease genes and variants (very comprehensive and open license)
 +
*[https://www.opentargets.org/ Open Targets] Another very comprehensive DB for disease target (mostly protein-coding genes) and related evidence
 +
*[http://denovo-db.gs.washington.edu/denovo-db/ denovo-db] a compendium of human de novo variants
 +
*[http://diseases.jensenlab.org/ DISEASES] gene-disease association from text mining (GHR, Uniprot, textmining)
 +
*[https://ghr.nlm.nih.gov/ GHR] Genetics Home Reference (by NCBI)
 +
*[http://disease-ontology.org/ Disease Ontology] Disease ontology files [http://django.nubic.northwestern.edu/fundo/ FUNDO] DOLite_term-to-genes map
 +
*[http://www.human-phenotype-ontology.org/ Human Phenotype Ontology]
 +
*[http://www.omim.org/ OMIM] Human disease DB (needs License to distribute)
 +
*[http://www.orphadata.org OrphaData] Open database for rare diseases and orphan drug (by Orphanet)
 +
*[http://geneticassociationdb.nih.gov/ GAD] Genetic Association Database: archive of human genetic association studies of complex diseases and disorders (includes summary data extracted from published candidate gene and GWAS studies).
 +
*[http://www.nlm.nih.gov/research/umls/ UMLS] Unified Medical Language Systems
 +
*[http://www.who.int/classifications/icd/en/ ICD] International Classification of Disease by WHO
 +
*[http://dga.nubic.northwestern.edu DGA] Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
 +
*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen datasets
 +
*[http://ogeedb.embl.de OGEE] Online GEne Essentiality database
 +
*[http://www.informatics.jax.org/humanDisease.shtml Human-Mouse Disease Connection] a part of MGI
 +
 
 +
- QTL depositories
 
*[https://www.gtexportal.org/home/ GTEx Portal] eQTL for ~50 different tissue types in humans
 
*[https://www.gtexportal.org/home/ GTEx Portal] eQTL for ~50 different tissue types in humans
 +
 +
- GWAS resources
 +
*[http://www.ncbi.nlm.nih.gov/gap/phegeni PheGenI] Phenotype-Genotype Integrator: For a query trait, it return GWAS loci collected from all available data resources (very convenient to make a single GWAS data set for each trait)
 
*[http://www.ebi.ac.uk/gwas/ GWAS catalog] Disease-associated variants; Now providing GWAS summary stat data
 
*[http://www.ebi.ac.uk/gwas/ GWAS catalog] Disease-associated variants; Now providing GWAS summary stat data
 +
*[http://ldsc.broadinstitute.org/ldhub/ LDHUB] a centralized database of summary-level GWAS results
 +
*[http://apps.nhlbi.nih.gov/Grasp/ Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP)] Better than GWAS catalog, including eQTL,QTLs
 +
*[http://jjwanglab.org:8080/gwasdb/ GWASdb] includes moderate SNPs (p-value < 10^-3) with manual curation from original papers; manually mapped ~1600 GWAS traits to ~500 HPO terms, ~440 DO terms, ~230 DOLite terms
 +
*[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks
 +
 +
- Genotype raw data depositories
 +
*[http://www.humanfunctionalgenomics.org Human Functional Genomics Project] Raw data are available from [https://hfgp.bbmri.nl/ BBMRI-NL data infrastructure]
 +
*[http://www.ukbiobank.ac.uk/ UK Biobank] Genotype and extensive phenotype data for ~500k UK people
 +
*[https://www.ebi.ac.uk/ega/ European Genome-phenome Archive(EGA)] Raw data of GWAS, WGS, Exome-seq. A great resource for meta-analysis
 +
*[http://www.ncbi.nlm.nih.gov/gap dbGaP] The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...)
 +
 +
- Clinical/Disease variant databases
 
*[http://research.nhgri.nih.gov/CGD/ CGD] Clinical Genomic Database
 
*[http://research.nhgri.nih.gov/CGD/ CGD] Clinical Genomic Database
 
*[http://www.hgmd.org/ HGMD] The human gene mutation database (The professional version of DB is commercial. The public version of DB is not downloadable.)
 
*[http://www.hgmd.org/ HGMD] The human gene mutation database (The professional version of DB is commercial. The public version of DB is not downloadable.)
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*[http://rcgdb.bioinf.uni-sb.de/MutomeWeb/ Roche Cancer Genome Database (RCGDB)] Germline/somatic mutations for cancer collected from diverse resourses (not downloadable)
 
*[http://rcgdb.bioinf.uni-sb.de/MutomeWeb/ Roche Cancer Genome Database (RCGDB)] Germline/somatic mutations for cancer collected from diverse resourses (not downloadable)
 
*[http://bioinf.uta.fi/base_root/ IDbase] Human Immunodeficiency-causing mutation database
 
*[http://bioinf.uta.fi/base_root/ IDbase] Human Immunodeficiency-causing mutation database
*[http://www.ukbiobank.ac.uk/ UK Biobank] Genotype and extensive phenotype data for ~500k UK people
 
*[http://jjwanglab.org:8080/gwasdb/ GWASdb] includes moderate SNPs (p-value < 10^-3) with manual curation from original papers; manually mapped ~1600 GWAS traits to ~500 HPO terms, ~440 DO terms, ~230 DOLite terms
 
*[https://www.ebi.ac.uk/ega/ European Genome-phenome Archive(EGA)] Raw data of GWAS, WGS, Exome-seq. A great resource for meta-analysis
 
*[http://www.ncbi.nlm.nih.gov/gap dbGaP] The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...)
 
 
*[http://www.ncbi.nlm.nih.gov/clinvar/ NCBI ClinVar] human variations and their relations to the human health (Not includes unreviewed data from GWAS)
 
*[http://www.ncbi.nlm.nih.gov/clinvar/ NCBI ClinVar] human variations and their relations to the human health (Not includes unreviewed data from GWAS)
*[http://www.ncbi.nlm.nih.gov/gap/phegeni PheGenI] Phenotype-Genotype Integrator
+
 
*[http://apps.nhlbi.nih.gov/Grasp/ Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP)] Better than GWAS catalog, including eQTL,QTLs
+
- Others
 
*[http://www.nature.com/icogs/ COGS nature resources] CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers.
 
*[http://www.nature.com/icogs/ COGS nature resources] CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers.
*[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks
 
 
*[http://www.personalgenomes.org/ Personal Genome Project]
 
*[http://www.personalgenomes.org/ Personal Genome Project]
*[http://www.humanfunctionalgenomics.org Human Functional Genomics Project] Raw data are available from [https://hfgp.bbmri.nl/ BBMRI-NL data infrastructure]
 
*[http://www.ncbi.nlm.nih.gov/gtex/GTEX2/gtex.cgi NCBI GTex(Genotype-Tissue Expression) browser] eQTL data download and analysis
 
*[https://www.med.unc.edu/pgc/downloads PGC GWAS rawdata download] contains links for other GWAS raw data
 
 
*[https://decipher.sanger.ac.uk/ DECIPHER] Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research)
 
*[https://decipher.sanger.ac.uk/ DECIPHER] Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research)
  
== Human Pathway/Signature genes and Interactome DBs ==
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== Interactome, Pathway/Signature Resources ==
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- Interactome DBs
 +
*[http://wodaklab.org/iRefWeb/ iRefWeb] a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
 +
*[http://string-db.org/ STRING] Known and predicted PPI
 +
*[http://interactome.baderlab.org/ Human Reference Interactome Project] Y2H-based human protein interactions
 +
 
 
- Pathway DBs
 
- Pathway DBs
 
*[http://pathguide.org/ Pathguide.org] A very comprehensive list of pathway and network databases
 
*[http://pathguide.org/ Pathguide.org] A very comprehensive list of pathway and network databases
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- Signature Gene Set DBs
 
- Signature Gene Set DBs
 
*[http://software.broadinstitute.org/gsea/msigdb MsigDB] License required for redistribution
 
*[http://software.broadinstitute.org/gsea/msigdb MsigDB] License required for redistribution
*[http://www.genesigdb.org/genesigdb/ GeneSigDB]
+
*[http://www.genesigdb.org/genesigdb/ GeneSigDB] Manually curated gene sets from Pubmed literature
 +
*[https://www.immunespace.org/announcements/home/thread.view?rowId=50 ImmnuneSigDB] Compendium of immune signatures (now available from MsigDB)
 +
*[http://biocc.hrbmu.edu.cn/CancerSEA/goDownload CancerSEA] which provides 14 signature profiles for characterization of cancer cells
 
*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
 
*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
 
*[http://amp.pharm.mssm.edu/L1000CDS2/help/ L1000CDS2] Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method
 
*[http://amp.pharm.mssm.edu/L1000CDS2/help/ L1000CDS2] Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method
 
*[http://amp.pharm.mssm.edu/creeds/ CREEDS] CRowd Extracted Expression of Differential Signatures: Signature gene sets from GEO selected by crowdsourcing project using CD method
 
*[http://amp.pharm.mssm.edu/creeds/ CREEDS] CRowd Extracted Expression of Differential Signatures: Signature gene sets from GEO selected by crowdsourcing project using CD method
  
- Interactome DBs
+
== Regulome Resources ==
*[http://wodaklab.org/iRefWeb/ iRefWeb] a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
+
- TF and motif DB
*[http://string-db.org/ STRING] Known and predicted PPI
+
*[http://humantfs.ccbr.utoronto.ca/ The Human Transcription Factors] 2765 putative TFs and 1639 confident TFs by manual curation
*[http://interactome.baderlab.org/ Human Reference Interactome Project] Y2H-based human protein interactions
+
*[http://cisbp.ccbr.utoronto.ca/ CIS-BP (Catalog of Inferred Sequence Binding Preferences)] >300 species, >250 TF families, >160,000 TFs. CisBP collects data from >25 sources, including other database such as [http://autosome.ru/HOCOMOCO/ HOCOMOCO] [http://jaspar.genereg.net JASPAR] [http://the_brain.bwh.harvard.edu/uniprobe/ UNIPROBE] [http://www.gene-regulation.com/pub/databases.html TRANSFAC]
  
== Epigenome and Cistrome Resources ==
 
 
- Epigenomics Consortium projects
 
- Epigenomics Consortium projects
*[http://genome.ucsc.edu/ENCODE/ ENCODE] Encyclopedia of DNA Elements project (human)
+
*[https://www.encodeproject.org/ ENCODE] Encyclopedia of DNA Elements project portal
 
*[http://www.roadmapepigenomics.org/ Road map Epigenomics] NIH Roda map Epigenomics project home
 
*[http://www.roadmapepigenomics.org/ Road map Epigenomics] NIH Roda map Epigenomics project home
 
*[http://ihec-epigenomes.org/ International Human Epigenome Consortium (IHEC)] The umbrella organization for international epigenomic efforts
 
*[http://ihec-epigenomes.org/ International Human Epigenome Consortium (IHEC)] The umbrella organization for international epigenomic efforts
 
*[http://www.4dnucleome.org/ 4D Nucleome] To understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension)   
 
*[http://www.4dnucleome.org/ 4D Nucleome] To understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension)   
 
- TF binding motif DB
 
*[http://cisbp.ccbr.utoronto.ca/ CIS-BP (Catalog of Inferred Sequence Binding Preferences)] >300 species, >250 TF families, >160,000 TFs. CisBP collects data from >25 sources, including other database such as [http://autosome.ru/HOCOMOCO/ HOCOMOCO] [http://jaspar.genereg.net JASPAR] [http://the_brain.bwh.harvard.edu/uniprobe/ UNIPROBE] [http://www.gene-regulation.com/pub/databases.html TRANSFAC]
 
  
 
- Promoter DB
 
- Promoter DB
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*[http://enhanceratlas.org/ Enhancer Atlas] Human enhancers based on >=3 independent high-throughput experimental datasets (contains 2,534,123 enhancers for 76 cell lines and 29 tissues)
 
*[http://enhanceratlas.org/ Enhancer Atlas] Human enhancers based on >=3 independent high-throughput experimental datasets (contains 2,534,123 enhancers for 76 cell lines and 29 tissues)
 
*[http://bioinfo.au.tsinghua.edu.cn/dbsuper/ dbSUPER] contains 82,234 super-enhancers in 102 human and 25 mouse tissue/cell types
 
*[http://bioinfo.au.tsinghua.edu.cn/dbsuper/ dbSUPER] contains 82,234 super-enhancers in 102 human and 25 mouse tissue/cell types
 +
*[http://zdzlab.einstein.yu.edu/1/hedd.php HEDD] Human Enhancer Disease Database (~2.8M enhancers from ENCODE, FANTOM5, RoadMap and annotations for disease, target, variant, conservation)
 +
*[http://biocc.hrbmu.edu.cn/DiseaseEnhancer/ DiseaseEnhancer] manual curation of disease-associated enhancers
  
 
- Transcriptional Start Site (TSS) DB
 
- Transcriptional Start Site (TSS) DB
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*[http://yiplab.cse.cuhk.edu.hk/jeme/ JEME] Computationally inferred EPI networks for 935 human primary cells, tissues, and cell lines
 
*[http://yiplab.cse.cuhk.edu.hk/jeme/ JEME] Computationally inferred EPI networks for 935 human primary cells, tissues, and cell lines
  
== miRNA Regulome Resources ==
 
 
- microRNA list and expression atlas
 
- microRNA list and expression atlas
 
*[http://mirbase.org// miRBase] miRNA database by Manchester University
 
*[http://mirbase.org// miRBase] miRNA database by Manchester University
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*[http://miRGator.kobic.re.kr miRGator] data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...  
 
*[http://miRGator.kobic.re.kr miRGator] data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...  
  
- Target prediction software
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- miRNA Target predictions
*[http://www.targetscan.org/ TargetScan] executable [http://genie.weizmann.ac.il/pubs/mir07/index.html PITA] executable [http://www.microrna.org/microrna/getDownloads.do miRanda] excecutable
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*[http://ophid.utoronto.ca/mirDIP/ mirDIP] >150M human miRNA-target predictions collected from 30 resources with integrative score
*[http://cegg.unige.ch/mirmap/ miRmap] target prediction by multiple algorithms, excecutable, precalculated, many other related data
+
*[http://mirdb.org/miRDB/ miRDB] Pre-calculated miRNA-target associations (based on SVM), not executable
+
  
 
- CLIP-seq database
 
- CLIP-seq database
 
*[http://starbase.sysu.edu.cn/ StarBase] DB for CLIP-seq data
 
*[http://starbase.sysu.edu.cn/ StarBase] DB for CLIP-seq data
  
== lncRNA Regulome Resources ==
+
- lncRNA Resources
 
*[http://fantom.gsc.riken.jp/cat/ FANTOM-CAT] An atlas of human long non-coding RNAs with accurate 5' ends
 
*[http://fantom.gsc.riken.jp/cat/ FANTOM-CAT] An atlas of human long non-coding RNAs with accurate 5' ends
 
*[http://www.noncode.org/ NONCODE] Integrative annotation of long noncoding RNAs
 
*[http://www.noncode.org/ NONCODE] Integrative annotation of long noncoding RNAs
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*[http://210.46.80.146/lincsnp/ LincSNP] a DB of disease-associated SNP in human lncRNA and their TFBS
 
*[http://210.46.80.146/lincsnp/ LincSNP] a DB of disease-associated SNP in human lncRNA and their TFBS
 
*[http://lulab.life.tsinghua.edu.cn/postar/ POSTAR] a DB of RNA binding protein binding sites in human and mouse transcriptome (experimental and computational methods)
 
*[http://lulab.life.tsinghua.edu.cn/postar/ POSTAR] a DB of RNA binding protein binding sites in human and mouse transcriptome (experimental and computational methods)
 
== Transcriptome Resources ==
 
- Data deposit servers
 
*[http://www.ncbi.nlm.nih.gov/sra SRA] Sequence Read Archive by NCBI
 
*[http://www.ebi.ac.uk/ena/ ENA] European Neucleotice Archive by EBI
 
*[http://www.ncbi.nlm.nih.gov/geo/ GEO] Gene Expression Omnibus (for processed data only)
 
*[http://www.weigelworld.org/resources/microarray/AtGenExpress/ AtGenExpress] Arabidopsis gene expression DB by Weigel lab (there are unpublished non-GEO data here)
 
*[http://www.immgen.org/ ImmGen] Immunological Genome Project [http://www.immgen.org/ModsRegs/modules.html Ontogenet] TF-module networks based on ImmGen data
 
 
- Expression Atlas
 
*[http://tissues.jensenlab.org/ TISSUE] Tissue Expression Database based on text mining (by Lars Jensen)
 
*[http://www.ebi.ac.uk/gxa/ EBI Gene Expression Atlas] Gene expression atlas for many organisms collected from various experiments
 
*[http://www.ebi.ac.uk/gxa/array/U133A Human Cell/tissue-specific gene expression map] for 369 different cell and tissue types with 5,372 human samples from GEO
 
*[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30611 Illumina Human Body Map Project (HBM)] RNA-seq data for 16 human tissue
 
*[http://www.informatics.jax.org/expression.shtml GXD] The mouse Gene Expression Database (by MGI)
 
  
 
== Single Cell Genomics Resources ==  
 
== Single Cell Genomics Resources ==  
*[https://github.com/seandavi/awesome-single-cell Awesome single cell] List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc (GitHub)
+
- DB for scRNA-seq data analysis tools
 +
*[https://github.com/seandavi/awesome-single-cell Awesome single cell]  
 +
*[https://www.scrna-tools.org/ scRNA-tools DB]
 +
- DB for scRNA-seq data
 
*[https://portals.broadinstitute.org/single_cell Single Cell Portal] scRNA-seq database by Broad Institute
 
*[https://portals.broadinstitute.org/single_cell Single Cell Portal] scRNA-seq database by Broad Institute
 
*[https://bioinfo.uth.edu/scrnaseqdb/ scRNASeqDB] scRNA-seq database by UTHSC
 
*[https://bioinfo.uth.edu/scrnaseqdb/ scRNASeqDB] scRNA-seq database by UTHSC
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*[http://single-cell.clst.riken.jp/ SCPortalen] human and mouse single-cell centric database
 
*[http://single-cell.clst.riken.jp/ SCPortalen] human and mouse single-cell centric database
 
*[https://support.10xgenomics.com/single-cell-gene-expression/datasets 10X Genomics Datasets] by 10X Genomics
 
*[https://support.10xgenomics.com/single-cell-gene-expression/datasets 10X Genomics Datasets] by 10X Genomics
 
== Phenome/Diseasome Resources ==
 
*[http://www.disgenet.org/web/DisGeNET DisGeNET] MetaDB for disease genes and variants (very comprehensive and open license)
 
*[https://www.opentargets.org/ Open Targets] Another very comprehensive DB for disease target (mostly protein coding genes) and related evidence
 
*[http://denovo-db.gs.washington.edu/denovo-db/ denovo-db] a compendium of human de novo variants
 
*[http://diseases.jensenlab.org/ DISEASES] gene-disease association from text mining (GHR, Uniprot, textmining)
 
*[https://ghr.nlm.nih.gov/ GHR] Genetics Home Reference (by NCBI)
 
*[http://disease-ontology.org/ Disease Ontology] Disease ontology files [http://django.nubic.northwestern.edu/fundo/ FUNDO] DOLite_term-to-genes map
 
*[http://www.human-phenotype-ontology.org/ Human Phenotype Ontology]
 
*[http://www.omim.org/ OMIM] Human disease DB (needs License to distribute)
 
*[http://www.orphadata.org OrphaData] Open database for rare diseases and orphan drug (by Orphanet)
 
*[http://geneticassociationdb.nih.gov/ GAD] Genetic Associationan Database: archive of human genetic association studies of complex diseases and disorders (includes summary data extracted from published candidate gene and GWAS studies).
 
*[http://www.nlm.nih.gov/research/umls/ UMLS] Unified Medical Language Systems
 
*[http://www.who.int/classifications/icd/en/ ICD] International Classification of Disease by WHO
 
*[http://dga.nubic.northwestern.edu DGA] Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
 
*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen data sets
 
*[http://ogeedb.embl.de OGEE] Online GEne Essentiality database
 
*[http://www.informatics.jax.org/humanDisease.shtml Human-Mouse Disease Connection] a part of MGI
 
  
 
==Chemical Biology and Drug Research Resources==
 
==Chemical Biology and Drug Research Resources==
 
- Drug and Bioactive chemical DBs
 
- Drug and Bioactive chemical DBs
 +
*[https://clue.io/repurposing Drug Repurposing Hub] a best-in-class drug screening collection of >3,000 clinical drugs and their annotation (structure, MoA, protein targets)
 
*[http://drugable.com/ Drugable.com] by National Library of Medicine, ~1 million chemicals, ~7000 structural pockets, ~4 millions of drug-protein interactions by docking model
 
*[http://drugable.com/ Drugable.com] by National Library of Medicine, ~1 million chemicals, ~7000 structural pockets, ~4 millions of drug-protein interactions by docking model
 
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] A DB contains drug structure and function by NCBI
 
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] A DB contains drug structure and function by NCBI
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*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
 
*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
 
*[https://clue.io/ CLUE] The expanded CMap including 1.3M L1000 profiles for 27,927 perturbagens (476,251 expressions)  
 
*[https://clue.io/ CLUE] The expanded CMap including 1.3M L1000 profiles for 27,927 perturbagens (476,251 expressions)  
 +
*[http://www.ilincs.org iLINCS] Integrated System to Analyze LINCS and other data
 
*[https://www.broadinstitute.org/cmap/ Connectivity Map (CMap)]  7,000 expression profiles representing 1,309 compounds
 
*[https://www.broadinstitute.org/cmap/ Connectivity Map (CMap)]  7,000 expression profiles representing 1,309 compounds
*[http://lincscloud.org/ LINCS] Library of Integrated Network-based Cellular Signatures (former Connectivity Map)
 
 
*[http://ctd.mdibl.org/ The Comparative Toxicogenomics database(CTD)] The major DB of chemical-disease links from literature curation  
 
*[http://ctd.mdibl.org/ The Comparative Toxicogenomics database(CTD)] The major DB of chemical-disease links from literature curation  
 
*[http://toxico.nibio.go.jp/english/index.html TG-GATE] Toxicogenomics data for >150 chemicals in rats and the primary cultured hepatocytes of rats and humans
 
*[http://toxico.nibio.go.jp/english/index.html TG-GATE] Toxicogenomics data for >150 chemicals in rats and the primary cultured hepatocytes of rats and humans
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== Cancer Biology Resources  ==
 
== Cancer Biology Resources  ==
 +
- Cancer Somatic Mutations DBs
 +
*[http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ COSMIC(The Catalog Of Somatic Mutations In Cancer)] By Sanger with expert curation
 +
*[http://docm.info DoCM] A database of functional variants validated in cancer
 +
*[http://civicdb.org CIViC] A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer
 +
 +
- Cancer Somatic Mutation Visualization
 +
*[https://pecan.stjude.cloud/proteinpaint Proteinpaint] Exploring genomic alteration in pediatric cancer
 +
 +
- Cancer Gene DBs
 +
*[http://cancer.sanger.ac.uk/cancergenome/projects/census/ CGC(Cancer Gene Census}] A catalog of genes with mutations that are causally implicated in cancer (by COSMIC)
 +
*[https://www.ncbi.nlm.nih.gov/pubmed/23539594 125 mutation-based drivers] see Supple TableS2A (71 TSG and 54 OG by 20/20 rule)
 +
*[https://bioinfo.uth.edu/TSGene/ TSGene] Literature-curated 1217 human TSGs (1018 protein-coding and 199 non-coding genes) and 320 protein-coding oncogenes
 +
*[http://ccgd-starrlab.oit.umn.edu CCGD(Candidate Cancer Gene Database)]A database of cancer driver genes from transposon-based forward genetic screens in mice
 +
*[https://www.nature.com/articles/nrc2771 77 Cancer Genes by amplification and overexpression] see Supple TableS2
 +
*[http://ncg.kcl.ac.uk/ NCG(The Network of Cancer Genes)] (~500) CGC + (~1000) Candidate genes from Panel Seq, WES, WGS studies
 +
 
- Cancer Genomics Research Gateway
 
- Cancer Genomics Research Gateway
*[https://ocg.cancer.gov/ NCI Office of Cancer Genomics] OCG is dedicated to supporting cancer genomics research by sharing molecular data from its programs to enhance understanding of cancer.
 
 
*[https://gdc.cancer.gov/ NCI Genomic Data Commons] GDC provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies.
 
*[https://gdc.cancer.gov/ NCI Genomic Data Commons] GDC provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies.
 +
*[https://dcc.icgc.org/ ICGC data portal] raw data from '''ICGC''' and '''TCGA'''
 +
*[https://ocg.cancer.gov/programs/target TARGET(Therapeutically Applicable Research To Generate Effective Treatments)] '''Childhood Cancer''' Genome Project by NCI
 +
*[https://www.pedpancan.com/pedpancan/ PedPanCan(A Pan-Cancer Study of '''Childhood Cancers''')] by Multi-Institutes including St. Jude Children's Research Hospital
 +
*[https://ocg.cancer.gov/ NCI Office of Cancer Genomics] OCG is dedicated to supporting cancer genomics research by sharing molecular data from its programs to enhance understanding of cancer.
 
*[https://ocg.cancer.gov/programs/ctd2/data-portal CTD2 data portal] Data Portal of [https://ocg.cancer.gov/programs/ctd2/overview Cancer Target Discovery and Development] program which strives to functionally validate discoveries from large-scale genomic initiatives.
 
*[https://ocg.cancer.gov/programs/ctd2/data-portal CTD2 data portal] Data Portal of [https://ocg.cancer.gov/programs/ctd2/overview Cancer Target Discovery and Development] program which strives to functionally validate discoveries from large-scale genomic initiatives.
*[https://dcc.icgc.org/ ICGC data portal] raw data from ICGC and TCGA
 
 
*[https://www.synapse.org/#!Synapse:syn7222066/wiki/405659 Synapse GENIE] The largest public cancer genome data by ACCR (see [http://www.aacr.org/Research/Research/Pages/aacr-project-genie.aspx#.WJv3szuLSUk ACCR GENIE project])   
 
*[https://www.synapse.org/#!Synapse:syn7222066/wiki/405659 Synapse GENIE] The largest public cancer genome data by ACCR (see [http://www.aacr.org/Research/Research/Pages/aacr-project-genie.aspx#.WJv3szuLSUk ACCR GENIE project])   
 
*[https://www.broadinstitute.org/software/cprg/ Cancer Program Resource Gateway] by Broad
 
*[https://www.broadinstitute.org/software/cprg/ Cancer Program Resource Gateway] by Broad
  
- Processed Genomics data and web server
+
- Cancer Genomics Data Analysis Cloud Platforms
*[http://www.cbioportal.org/ cBioPortal] Data sets from published studies including TCGA
+
*[http://cgc.systemsbiology.net/ ISB-CGC] Cancer Genomics Cloud by ISB
*[http://methhc.mbc.nctu.edu.tw/ MethHC] A database of DNA Methylation and gene expression in Human Cancer (use Pan-cancer data)
+
*[http://mev.tm4.org WebMeV] Analysis of large genomic data, particularly for RNASeq and microarray data (TCGA, GEO, or user-uploaded).
  
- Cancer Genome Analysis software
+
- Tumor Microenvironment Analysis tools
*[http://www.cravat.us/ CRAVAT] Cancer-Related Analysis of Variants ToolKit
+
*[https://cistrome.shinyapps.io/timer/ TIMER] Web server for a comprehensive TME analysis
*[http://www.intogen.org/ IntOGen] Integrative Onco Genomics
+
*[http://xcell.ucsf.edu/ xCell] Tumor cellular heterogeneity analysis web server; R package is also available from [https://github.com/dviraran/xCell github]
 
+
- Cancer genes and mutations DBs
+
*[http://cancer.sanger.ac.uk/cancergenome/projects/census/ CGC] Cancer Gene Census
+
*[http://bioinfo.mc.vanderbilt.edu/TSGene/ TSGene] Literature curated Tumor suppressor genes (~1000 coding, ~200 non-coding); v2 paper also provides ~300 oncogenes in Supple
+
*[http://ncg.kcl.ac.uk/ NCG] The Network of Cancer Genes; a manually curated repository of cancer genes from the literature (1571 cancer genes by v5)
+
*[http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ COSMIC] Catalog Of Somatic Mutations In Cancer
+
*[http://civicdb.org CIViC] A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer
+
*[http://docm.info DoCM] A database of curated mutations in cancer 
+
  
 
- Cancer Pharmacogenomics
 
- Cancer Pharmacogenomics
*[http://www.cancerrxgene.org/ Genomics of Drug Sensitivity in Cancer (GDSC)] The largest public DB for drug sensitivity of cancer cell line and biomarkers
+
*[https://pharmacodb.pmgenomics.ca/ PharmacoDB] Integrative database for cancer pharmacogenomics (CCLE, GDSC, CTRP, and more)
*[http://www.broadinstitute.org/ccle/home Cancer Cell line Encyclopedia (CCLE)] by Broad-Novartis, 1000 cancer cell lines, ~1200 compounds and their combinations
+
*[https://portals.broadinstitute.org/ctrp/ CTRP] The Cancer Therapeutics Response Portal (~550 drugs x ~890 cell lines)
 +
*[http://www.cancerrxgene.org/ Genomics of Drug Sensitivity in Cancer (GDSC)] (~250 drugs x ~1110 cell lines)
 +
*[http://www.broadinstitute.org/ccle/home Cancer Cell line Encyclopedia (CCLE)] (~20 drugs x ~1060 cell lines)
  
 
- Cancer cell essential genes
 
- Cancer cell essential genes
Line 250: Line 263:
 
*[http://www.broadinstitute.org/achilles Achilles Project] shRNA-based screen for 216 cancer cell lines (v2.4.3) and CRISPR-based screen for 33 cancer cell lines (v3.3.8)
 
*[http://www.broadinstitute.org/achilles Achilles Project] shRNA-based screen for 216 cancer cell lines (v2.4.3) and CRISPR-based screen for 33 cancer cell lines (v3.3.8)
 
*[http://colt.ccbr.utoronto.ca/cancer/ COLT-cancer database] shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines
 
*[http://colt.ccbr.utoronto.ca/cancer/ COLT-cancer database] shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines
 
- Data for survival predictions
 
*[https://www.synapse.org/#!Synapse:syn1710282 Synapse TCGA-Pancancer survival prediction] analysis-ready TCGA data for survival prediction
 
 
- Cancer Immunogenomics analysis tools
 
*[http://xcell.ucsf.edu/ xCell] Tumor cellular heterogeneity analysis web server; R package is also available from [https://github.com/dviraran/xCell github]
 
  
 
== Metagenome DBs and tools  ==
 
== Metagenome DBs and tools  ==
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*[http://www.metahit.eu/ MetaHIT] Metagenomics of the human intestinal tract
 
*[http://www.metahit.eu/ MetaHIT] Metagenomics of the human intestinal tract
 
*[http://huttenhower.sph.harvard.edu/ Huttenhower Lab] A great resource for analysis tools
 
*[http://huttenhower.sph.harvard.edu/ Huttenhower Lab] A great resource for analysis tools
 +
- Bacterial strain bank
 +
*[https://kctc.kribb.re.kr/kctc.aspx Korean Collection for Type Cultures]
 +
*[https://www.atcc.org/ ATCC]
  
 
== Proteome Resources ==
 
== Proteome Resources ==
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== Other Resources ==
 
== Other Resources ==
- Academic society
+
- Academic society & Research Center
 
*[http://www.ashg.org/ ASHG] American Society of Human Genetics
 
*[http://www.ashg.org/ ASHG] American Society of Human Genetics
 
*[http://www.aacr.org AACR] American Association for Cancer Research
 
*[http://www.aacr.org AACR] American Association for Cancer Research
 +
*[https://www.esmo.org/ ESMO] European Society of Medical Oncology
 
*[http://www.human-microbiome.org/ IHMC] The International Human Microbiome Consortium
 
*[http://www.human-microbiome.org/ IHMC] The International Human Microbiome Consortium
 
*[http://www.ksbi.or.kr/ KSBI] Korean Society of Bioinformatics
 
*[http://www.ksbi.or.kr/ KSBI] Korean Society of Bioinformatics
Line 297: Line 308:
 
*[http://www.ksmcb.or.kr/ KSMCB] Korean Society of Molecular and Cellular Biology
 
*[http://www.ksmcb.or.kr/ KSMCB] Korean Society of Molecular and Cellular Biology
 
*[http://new.ksbmb.or.kr/ KSBMB] Korean Society of Biochemistry and Molecular Biology
 
*[http://new.ksbmb.or.kr/ KSBMB] Korean Society of Biochemistry and Molecular Biology
 +
*[http://mrc-systemsmed.org/ Yonsei Medical Research Center for Systems Medicine]
  
 
- Cool software
 
- Cool software

Revision as of 21:34, 21 January 2019

Contents

Google DataSet Search Engine

Gene/Genome Annotations

  • CCDS The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation
  • GENCODE The Encyclopedia of Genes

Variome Resources

- Variation DBs

  • ExAC (Exome Aggregation Consortium) Exome variation data from >60k individuals
  • 1000 Genome Project Catalog of 60 million variant sites (SNV, CNV, SV), 2535 individuals from 26 populations
  • UK10K Sequencing 10,000 people (4,000 healthy, 6,000 disease) in England
  • Genomics England Sequencing 100,000 people in England focusing on patients with a rare disease and their families and patients with cancer.
  • DiscovEHR Collaboration between the Regeneron Genetics Center (WES) and Geisinger Health System (EHR) provides the vcf by 50,000 MyCode participants
  • European Variation Archive Most comprehensive and organized by studies (include Clinical variants)
  • NCBI Variation Variation DBs (dbSNP, dbVar, dbGaP, ClinVar)
  • iJGVD Integrative Japanese Genome Variation Database
  • HGV Database The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation

- Functional significance of variants

Phenome/Diseasome Resources

- Human Disease DBs

  • DisGeNET MetaDB for disease genes and variants (very comprehensive and open license)
  • Open Targets Another very comprehensive DB for disease target (mostly protein-coding genes) and related evidence
  • denovo-db a compendium of human de novo variants
  • DISEASES gene-disease association from text mining (GHR, Uniprot, textmining)
  • GHR Genetics Home Reference (by NCBI)
  • Disease Ontology Disease ontology files FUNDO DOLite_term-to-genes map
  • Human Phenotype Ontology
  • OMIM Human disease DB (needs License to distribute)
  • OrphaData Open database for rare diseases and orphan drug (by Orphanet)
  • GAD Genetic Association Database: archive of human genetic association studies of complex diseases and disorders (includes summary data extracted from published candidate gene and GWAS studies).
  • UMLS Unified Medical Language Systems
  • ICD International Classification of Disease by WHO
  • DGA Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
  • GenomeRNAi v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen datasets
  • OGEE Online GEne Essentiality database
  • Human-Mouse Disease Connection a part of MGI

- QTL depositories

  • GTEx Portal eQTL for ~50 different tissue types in humans

- GWAS resources

  • PheGenI Phenotype-Genotype Integrator: For a query trait, it return GWAS loci collected from all available data resources (very convenient to make a single GWAS data set for each trait)
  • GWAS catalog Disease-associated variants; Now providing GWAS summary stat data
  • LDHUB a centralized database of summary-level GWAS results
  • Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP) Better than GWAS catalog, including eQTL,QTLs
  • GWASdb includes moderate SNPs (p-value < 10^-3) with manual curation from original papers; manually mapped ~1600 GWAS traits to ~500 HPO terms, ~440 DO terms, ~230 DOLite terms
  • DistiLD Diseases and Traits in Linkage Disequilibrium Blocks

- Genotype raw data depositories

- Clinical/Disease variant databases

  • CGD Clinical Genomic Database
  • HGMD The human gene mutation database (The professional version of DB is commercial. The public version of DB is not downloadable.)
  • OMIM Germline mutations for genetic diseases
  • Roche Cancer Genome Database (RCGDB) Germline/somatic mutations for cancer collected from diverse resourses (not downloadable)
  • IDbase Human Immunodeficiency-causing mutation database
  • NCBI ClinVar human variations and their relations to the human health (Not includes unreviewed data from GWAS)

- Others

  • COGS nature resources CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers.
  • Personal Genome Project
  • DECIPHER Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research)

Interactome, Pathway/Signature Resources

- Interactome DBs

  • iRefWeb a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
  • STRING Known and predicted PPI
  • Human Reference Interactome Project Y2H-based human protein interactions

- Pathway DBs

  • Pathguide.org A very comprehensive list of pathway and network databases
  • Gene Ontology by Gene Ontology Consortium
  • KEGG pathways and many more
  • Biocyc includes Metacyc, Ecocyc, Humancyc, Aracyc, Yeastcyc
  • Reactome A manually curated and peer-reviewed pathway DB
  • Pathway Interaction Database (PID) Human pathways curated by NCI-Nature/imported from BioCarta/Reactome
  • CORUM Comprehensive Resource of Mammalian Protein Complexes
  • NetPath A database for signaling pathways (cancer/immune signaling pathways)
  • SIGNOR 11000 manually-annotated causal relationships between proteins that participate in signal transduction
  • UniProt-GOA by EBI (support multi-species annotation)
  • UniPathway a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc)

- Signature Gene Set DBs

  • MsigDB License required for redistribution
  • GeneSigDB Manually curated gene sets from Pubmed literature
  • ImmnuneSigDB Compendium of immune signatures (now available from MsigDB)
  • CancerSEA which provides 14 signature profiles for characterization of cancer cells
  • DSigDB Drug signature database for gene set analysis
  • L1000CDS2 Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method
  • CREEDS CRowd Extracted Expression of Differential Signatures: Signature gene sets from GEO selected by crowdsourcing project using CD method

Regulome Resources

- TF and motif DB

- Epigenomics Consortium projects

- Promoter DB

  • EPD Eukaryotic Promoter Database; Databases of experimentally validated (by either publication or in-house assay) promoters in various organisms

- Enhancer DB

  • Enhancer Atlas Human enhancers based on >=3 independent high-throughput experimental datasets (contains 2,534,123 enhancers for 76 cell lines and 29 tissues)
  • dbSUPER contains 82,234 super-enhancers in 102 human and 25 mouse tissue/cell types
  • HEDD Human Enhancer Disease Database (~2.8M enhancers from ENCODE, FANTOM5, RoadMap and annotations for disease, target, variant, conservation)
  • DiseaseEnhancer manual curation of disease-associated enhancers

- Transcriptional Start Site (TSS) DB

  • DBTTS contains 491 million TSS tag sequences for 20 tissues and 7 cell cultures in human and mouse

- Chip-seq/DNase-seq DB

  • Cistrome DB the most comprehensive DB for Chip-seq and DNase-seq data

- Enhancer-Promoter Interaction DB

  • JEME Computationally inferred EPI networks for 935 human primary cells, tissues, and cell lines

- microRNA list and expression atlas

  • miRBase miRNA database by Manchester University
  • microRNA.org download miRNA expression atlas for human, mouse, rat
  • microRNAome microRNA RNA-seq based atlas for 46 primary cell types and 42 cancer or immortalized cell lines

- microRNA-target links (Gold standard)

  • miRWalk2.0 Validated links from 4 databases and text minings, Predicted links from 13 prediction data sets
  • miRTarBase Experimental-based microRNA-target links (most popular)

- microRNA-disease

  • Human microRNA Disease Database(HMDD) Manually curated microRNA-disease links (most comprehensive)
  • PhenomiR DB for dysregulated miRNA in diseases
  • dbDEMC DB for dysregulated miRNA in Cancer
  • miRGator data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...

- miRNA Target predictions

  • mirDIP >150M human miRNA-target predictions collected from 30 resources with integrative score

- CLIP-seq database

- lncRNA Resources

  • FANTOM-CAT An atlas of human long non-coding RNAs with accurate 5' ends
  • NONCODE Integrative annotation of long noncoding RNAs
  • lncRNAdb a reference DB for long noncoding RNAs
  • RAIN RNA–protein Association and Interaction Networks Intro to RAIN
  • NPInter ncRNA interaction database (ncRNA and other molecules)
  • RAID RNA-associated interaction DB (very comprehensive)
  • LncRNADisease a DB for lncRNA associated diseases
  • ncFANs a web server for functional annotation of ncRNA
  • LincSNP a DB of disease-associated SNP in human lncRNA and their TFBS
  • POSTAR a DB of RNA binding protein binding sites in human and mouse transcriptome (experimental and computational methods)

Single Cell Genomics Resources

- DB for scRNA-seq data analysis tools

- DB for scRNA-seq data

  • Single Cell Portal scRNA-seq database by Broad Institute
  • scRNASeqDB scRNA-seq database by UTHSC
  • conquer A repository of consistently processed, analysis-ready single-cell RNA-seq data sets
  • Jinglebells A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level
  • SCPortalen human and mouse single-cell centric database
  • 10X Genomics Datasets by 10X Genomics

Chemical Biology and Drug Research Resources

- Drug and Bioactive chemical DBs

  • Drug Repurposing Hub a best-in-class drug screening collection of >3,000 clinical drugs and their annotation (structure, MoA, protein targets)
  • Drugable.com by National Library of Medicine, ~1 million chemicals, ~7000 structural pockets, ~4 millions of drug-protein interactions by docking model
  • PubChem A DB contains drug structure and function by NCBI
  • ChEMBL A DB contains drug structure and functions by EBI
  • Drugs@FDA A DB for FDA approved drugs
  • DailyMed High quality Information about marketed drugs by NCBI
  • SuperDrug A DB contains 3D-structures of drugs

- Clinical Trial Information

- Drug Target DBs

- Drug signature, Pharmacogenomics, Toxicogenomics DBs

- Drug-Gene Interaction DBs

  • MOSAIC Chemical-genetic interactions in Yeast (cover >13000 compounds)

Cancer Biology Resources

- Cancer Somatic Mutations DBs

- Cancer Somatic Mutation Visualization

  • Proteinpaint Exploring genomic alteration in pediatric cancer

- Cancer Gene DBs

- Cancer Genomics Research Gateway

- Cancer Genomics Data Analysis Cloud Platforms

  • ISB-CGC Cancer Genomics Cloud by ISB
  • WebMeV Analysis of large genomic data, particularly for RNASeq and microarray data (TCGA, GEO, or user-uploaded).

- Tumor Microenvironment Analysis tools

  • TIMER Web server for a comprehensive TME analysis
  • xCell Tumor cellular heterogeneity analysis web server; R package is also available from github

- Cancer Pharmacogenomics

- Cancer cell essential genes

  • GenomeCRISPR A database for high-throughput CRISPR/Cas9 screening experiments
  • Achilles Project shRNA-based screen for 216 cancer cell lines (v2.4.3) and CRISPR-based screen for 33 cancer cell lines (v3.3.8)
  • COLT-cancer database shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines

Metagenome DBs and tools

- Metagenomic data central DB

- Human microbiome

- Bacterial strain bank

Proteome Resources

- Human Proteome Database

  • Human Proteome Map 85 samples from 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues
  • ProteomicsDB >10,000 raw data files from 60 human tissues, 147 cell lines, and 13 body fluids
  • The Human Protein Atlas The tissue-based map of human proteome based on Immunohistochemistry (for 32 different tissues and organs)

- Open stand-alone software for mass spectra database search (search engines)

  • MSblender A combined search engine
  • MS-GFDB: Its successor MS-GF+ is faster and more sensitive for high-resolution MS data.
  • X!TANDEM
  • Comet: the direct descendant of Crux, which is an academic version of the commercial software SEQUEST
  • MyriMatch
  • OMSSA Due to budgetary constraints NCBI has discontinued OMSSA. Historical binaries are available from here.

- Protein localization and Secretome DB

  • Vesiclepedia A DB for all types of Extracellular Vesicles (includes Exocarta)
  • Exocarta A DB for Exosome
  • EVpedia A DB for Extracellular Vesicles with many analysis software

Other Resources

- Academic society & Research Center

  • ASHG American Society of Human Genetics
  • AACR American Association for Cancer Research
  • ESMO European Society of Medical Oncology
  • IHMC The International Human Microbiome Consortium
  • KSBI Korean Society of Bioinformatics
  • KCA Korean Cancer Association
  • KOGO Korea Genome Organization
  • KSMCB Korean Society of Molecular and Cellular Biology
  • KSBMB Korean Society of Biochemistry and Molecular Biology
  • Yonsei Medical Research Center for Systems Medicine

- Cool software

  • REVIGO Visualize GO enrichment summary
  • UpSetR Shiny App Visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries; R package is also available from github
  • VENNY Drawing Venn diagram

- Data-driven Omics companies

- Machine Learning

- Neuroscience

- Others

Personal tools
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